Attenuated forms of bovine viral diarrhea virus

ABSTRACT

The present invention is directed to a method of producing attenuated forms of bovine viral diarrhea (BVD) virus by mutating the N pro  protease gene. The invention includes the attenuated viruses made by the method, antibodies generated using these viruses, and vaccines that can be used for immunizing cattle.

This application is a division of Ser. No. 09/433,262, filed Nov. 4, 1999, now U.S. Pat. No. 6,168,942, which claimed the benefit of Ser. No. 60/107,908, filed Nov. 10, 1998.

FIELD OF THE INVENTION

The present invention is directed to methods of producing an attenuated form of bovine viral diarrhea (BVD) virus by inactivating a specific gene in the viral genome. The attenuated virus, or the mutated viral genome, can be used to produce antibody against BVD virus or in vaccines designed to protect cattle from viral infection.

BACKGROUND OF THE INVENTION

Bovine viral diarrhea (BVD) virus is classified in the pestivirus genus and Flaviviridae family. It is closely related to viruses causing border disease in sheep and classical swine fever. Infected cattle exhibit “mucosal disease” which is characterized by elevated temperature, diarrhea, coughing and ulcerations of the alimentary mucosa (Olafson, et al., Cornell Vet. 36:205-213 (1946); Ramsey, et al., North Am. Vet. 34:629-633 (1953)). The BVD virus is capable of crossing the placenta of pregnant cattle and may result in the birth of persistently infected (Pl) calves (Malmquist, J. Am. Vet. Med. Assoc. 152:753-768 (1968); Ross, et al., J. Am. Vet. Med. Assoc. 188:618-619 (1986)). These calves are immunotolerant to the virus and persistently viremic for the rest of their lives. They provide a source for outbreaks of mucosal disease (Liess, et al., Dtsch. Tieraerzti. Wschr. 81:481-487 (1974)) and are highly predisposed to infection with microorganisms causing diseases such as pneumonia or enteric disease (Barber, et al., Vet. Rec. 117:459-464 (1985)).

BVD viruses are classified as having one of two different biotypes. Those of the “cp” biotype induce a cytopathic effect in cultured cells, whereas viruses of the “ncp” biotype do not (Gillespie, et al., Cornell Vet. 50:73-79 (1960)). In addition, two major genotypes (type I and II) are recognized, both of which have been shown to cause a variety of clinical syndromes (Pellerin, et al., Virology 202:260-268 (1994); Ridpath, et al., Virology 205:66-74 (1994)).

The genome of the BVD virus is approximately 12.5 kb in length and contains a single open reading frame located between the 5′ and 3′ non-translated regions (NTRs) (Collett, et al. Virology 163:191-199 (1988)). A polyprotein of approximately 438 kD is transisted from this open reading frame and is processed into viral structural and nonstructural proteins by cellular and viral proteases (Tautz, et al., J. Virol. 71:5415-5422 (1997); Xu, et al., J. Virol. 71:5312-5322 (1997); Elbers, et al., J. Virol. 70:4131-4135 (1996); and Wiskerchen, et al., Virology 184:341-350 (1991)). Among the viral enzymes that participate in this processing are the proteases N^(pro) and NS3. N^(pro) is the first protein encoded by the viral open reading frame and cleaves itself from the rest of the synthesized polyprotein (Stark, et al., J. Virol. 67:7088-7093 (1993); Wiskerchen, et al., Virol. 65:4508-4514 (1991)).

Among the BVD vaccines that are currently available are those in which virus has been chemically inactivated (McClurkin, et al., Arch. Virol. 58:119 (1978); Fernelius, et al., Am. J. Vet. Res. 33:1421-1431 (1972); and Kolar, et al., Am. J. Vet. Res. 33:1415-1420 (1972)). These vaccines have typically required the administration of multiple doses in achieve primary immunization, provide immunity of short duration and do not protect against fetal transmission (Bolin, Vet. Clin, North Am. Food Anim. Pract. 11:615-625 (1995)). In sheep, a subunit vaccine based upon a purified E2 protein has been reported (Bruschka, et al., Vaccine 15:1940-1945 (1997)). Unfortunately, only one such vaccine appears to protect fetuses from infection and this protection is limited to one strain of homologous virus. There is no correlation between antibody titers and protection from viral infection.

In addition, modified live virus (MLV) vaccines have been produced using BVD virus that has been attenuated by repeated passage in bovine or porcine cells (Coggins, et al. Cornell Vet. 51:539 (1961); and Phillips, et al., Am. J. Vet. Res. 36:135 (1975)) or by chemically induced mutations that confer a temperature-sensitive phenotype on the virus (Lobmann, et al., Am. J. Vet. Res. 45:2498 (1954); and Lobmann, et al., Am. J. Vet. Res. 47:557-561 (1986)). A single dose of MLV vaccine has proven sufficient for immunization and the duration of immunity can extend for years in vaccinated cattle (Coria, et al., Can. J. Con. Med. 42:239 (1978)). In addition, cross-protection has been reported from calves vaccinated with MLV-type vaccines (Martin, et al., In Proceedings of the Conference Res. Workers' Anim. Dis., 75:183 (1994)). However, safety considerations, such as possible fetal transmission of the virus, have been a major concern with respect to the use of these vaccines (Bolin, Vet. Clin. North Am. Food Anim. Pract. 11:615-625 (1995)).

A clear need exists for near and effective vaccines to control the spread of the BVD virus. Given that the disease caused by this virus is one of the most widespread and economically important diseases of cattle, such vaccines would represent a substantial advance in livestock farming.

SUMMARY OF THE INVENTION

The present invention is based upon the discovery that attenuated forms of BVD virus can be produced by deleting or inactivating the N^(pro) protease gene. These viruses are much less infectious than their wild-type counterparts in bovine cell lines and are suitable for use in vaccines for cattle. A complete genomic sequence of one such attenuated virus is disclosed herein, and a plasmid encoding this virus, i.e. pBVDdN1, has been deposited with the American Type Culture Collection (ATCC) as ATCC No. 203354.

A. Compositions and Methods Based Upon the BVDdN1 Attenuated Virus

In its first aspect, the present invention is based upon the development of a specific attenuated BVD viral strain. The strain is produced by mutating a wild type viral genome to delete the N^(pro) protease gene and its full-length sequence is shown in SEQ ID NO:1 and FIG. 2, from nt 39 to nt 12116. Thus, the invention is directed to a virus having a genomic sequence comprising that shown, and preferably consisting essentially of that shown. Ordinarily, the BVD virus has a genome in the form of RNA. When cloned, this will more typically be in the form of DNA. Unless otherwise indicated, the term “nucleic acid” refers to both BVD viral DNA and RNA sequences. For convenience, sequence listing entries only show DNA sequences but the corresponding RNA sequence for each will be readily apparent to those of skill in the art. The term “consisting essentially of” refers to sequences that are substantially the same as those specified both in terms of structure and function. Thus, the invention includes not only the sequences expressly depicted, but also corresponding sequences made by introducing insubstantial additions or substitutions. In particular, the invention includes degenerate nucleic acid sequences that encode the same BVD proteins as SEQ ID NO:1. This particular sequence, i.e., SEQ ID NO:1 from nt 39 to nt 12116, and the corresponding virus it encodes have, for convenience, been designated as the “BVDdN1” genome and virus. Virus can be present either as part of a larger preparation or in substantially purified form, i.e., in a form essentially free from any other viral types.

The invention includes host cells carrying a BVDdN1 nucleic acid molecule of the present invention. The term “host cells” is meant to include any procaryotic cells carrying a BVDdN1 nucleic acid molecule, and any eukarylotic cells infected with the virus or otherwise carrying a BVDdN1 nucleic acid molecule. For prokaryolic cells, the STBL2 strain of E. coli (GibcoBRL) has been found to give the best results for propagating the plasmid, and is generally preferred. For eukaryotic cells, mammalian cells such as MDBK cells (ATCC CCL-22) and RD cells (stable transformed bovine testicular cells) are generally preferred. However, other cultured cells can be used as well. The invention further includes progeny virus produced in such host cells.

The BVDdN1 virus can be used to induce the production of antibody by infecting an animal at an effective dosage, i.e., at a dosage high enough to provoka antibody production. The antibodies can be made in any of the animals normally used for this purpose (such as mice, rabbits, goats, or sheep) but, preferably, antibodies will be made in cattle. The term “antibody to BVD virus” as used herein refers to antibodies that reach preferentially in the sense of having at least a 100-fold greater affinity for a strain of BVD virus than for any other, non-BVD virus. Although not preferred, virus can be further inactivated prior to administration to an animal using chemical treatments involving agents such as formalin, paraformaldehyde, phenol, lactopropionate, psoralens, platinum complexes, ozone or other viricidal agents. Antibodies made by these procedures are themselves included within the scope of the invention and can be isolated using techniques that are well known in the art (see e.g., Harlow, et al., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, N.Y. (1988)). The antibodies can be used, inter alia, in methods designed to detect the presence of BVD in biological or laboratory samples.

In another aspect, the invention is directed in a vaccine comprising the BVDdN1 virus and a veterinarily acceptable carrier. This vaccine can includes any of the adjuvants and other agents typically used in such preparations. An immune response can be induced in cattle by administering the vaccine at a dosage sufficient to induce protective immunity against subsequent challenge with BVD virus. Typically, the vaccine will be administered parenterally, but other routes of administration are compatible with the invention as well. If necessary, two or more inoculations can be given at regular intervals of, for example, two to eight weeks. Standard procedures well known in the art can be used in optimize immunization protocols.

B. Compositions and Methods Based Upon BVDdN1 Genomic Nucleic Acid

Recent work has demonstrated that it is possible to prepare effective vaccines by injecting animals with nucleic acids encoding immunogens. Methods for making and administering these “DNA vaccines” have been described in detail (see e.g., U.S. Pat. Nos. 5,589,466; 5,580,859; and 5,703,055) and can be applied to BVDdN1 genomic nucleic acid. Thus, in another aspect, the present invention is directed to a nucleic acid molecule, preferably in substantially purified form, comprising the sequence of SEQ ID NO:1, from nt 39 to nt 12116, or a degenerate variant thereof. In a preferred embodiment, the present invention is directed to a nucleic acid molecule, preferably in substantially purified form, consisting essentially of the sequence of SEQ ID NO:1, from nt 39 to nt 12116. As used herein, “substantially purified” refers to a desired product that is essentially free from contaminating materials. For example, a “substantially purified” nucleic acid molecule would be essentially free from other contaminating nucleic acid molecules and typically comprise at least 85 wt % of the nucleic acid molecules in a sample, with greater percentages being preferred. One method for determining the purity of a nucleic acid is by electrophoresting a preparation in a matrix such as polyacrylamide or agarose. Purity is evidenced by the appearance of a single band after staining. Other methods for assessing purify include chromatography and analytical centrifugation.

The BVDdN1 genomic nucleic acid can be incorporated into a vector as a distinct coding element. The phrase “distinct coding element” refers to the portion of the vector that is translated into viral polypeptide and, eventually, virus. It is distinct in the sense that it does not include any other translated elements that would substantially alter the BVDdN1 product. This vector, or the BVDdN1 nucleic acid itself, can be used to transfect a host cell in order to produce progeny attenuated virus.

The invention also includes methods of inducing the production of antibody to BVD virus by injecting the BVDdN1 nucleic acid, or a vector containing this nucleic acid, directly into an animal. Any animal capable of making antibody can be used, but cattle are generally preferred. Antibody made in this way is part of the invention and can be purified from animals and used, for example, in assays designed to detect the presence of BVD virus in culture medium or biological fluid.

Vaccines for administration to cattle can be prepared based upon the BVDdN1 genomic nucleic acid (see references cited supra), in combination with a veterinarily acceptable carrier, and used in immunization protocols optimized for inducing protective immunity against subsequent viral infection.

C. Methods of Mutating Wild Type BVD Genomes

In a more general sense, the present invention is directed to a method of modifying a genome from a substantially purified wild type BVD virus in such a manner as to make it suitable for use in a vaccine. The term “substantially purified” as used in this contact refers to a viral preparation consisting, preferably, of a single strain of BVD virus with no other types of virus being present. The main distinguishing feature of the procedure is that the genomic nucleic acid is mutated to inactivate the N^(pro) protease gene. In this context, a gene is considered to be inactivated either if no product is made (for example, the gene is deleted), or a product a made that can no longer carry out its normal biological function (e.g., proteolytic cleavage), or a product is made that carries out its normal biological function but at a significantly reduced rate. Any method that results in the inactivation of the N^(pro) protease can be used. For example, genomic RNA can be isolated from the wild type BVD virus, reverse transcribed to form cDNA and then cloned using standard procedures. Mutations can then be introduced into the N^(pro) protease gene by procedures such as the polymerase chain reaction (PCR), site directed mutagenesis, by synthesizing and ligating DNA fragments in such a manner that N^(pro) is partially or completely eliminated, or by random mutagenesis techniques including, e.g., exposure to a chemical mutagen or radiation as known in the art, or by a combination of such procedures.

Once the BVD viral genome has been modified so that the N^(pro) gene is inactivated, it can be cloned into an appropriate vector and produced in large amounts. As discussed above, vectors should include the BVD sequence as a distinct element with a sequence comprising, or consisting essentially of, that of the mutated wild type virus. Either the mutated BVD genome or the vector comprising the genome can be transformed or transfected into a host cell for the purpose of making either large amounts of viral nucleic acid or virus itself.

As discussed above in connection with the BVDdN1 genomic DNA, antibody to BVD virus can be produced in an animal by administering any wild type BVD viral genome that has been mutated in the manner discussed above. In general, it is preferred that antibody production take place in cattle, but other animals can be used as well.

Vaccines incorporating the mutated BVD genomic nucleic acid can be produced and used to induce an immune response in cattle using standard DNA immunization procedures (e.g., those discussed in U.S. Pat. Nos. 5,589,466; 5,580,859; and 5,703,055). The vaccines, antibodies, and nucleic acids made by the methods discussed herein are all part of the present invention.

D. Methods of Making Attenuated BVD Virus

It has been discovered that when the nucleic acid of a BVD virus is mutated so as to inactivate the N^(pro) protease gene, an attenuated virus is produced that is much less infectious in cell culture. The relatively slow replication of these attenuated viruses allows animals to marshal their immunological defenses in a way that is not possible for a rapidly propagating wild type virus. Thus, the methods for producing a mutated viral genome discussed above for BVDdN1 lead directly to a general method for attenuating BVD virus so as to make it suitable for use in a vaccine. In general, the procedure involves isolating a wild type BVD virus; cloning its genomic nucleic acid; mutating the cloned nucleic acid so as to inactivate the N^(pro) protease gene; and then transforming or transfecting the mutated nucleic acid into a host to produce the attenuated virus. Although any of the methods discussed above for producing mutations can be used, the preferred method will be to delete at or part of the N^(pro) protease gene.

The present invention encompasses not only methods for making attenuated virus, but also the virus itself, host cells infected with the virus and progeny virus produced by these host cells. Antibody can be made to the attenuated BVD virus by infecting animals, preferably cattle, at an effective dosage. Antibodies made in this manner are part of the invention and can be isolated and used in diagnostic procedures, or for detecting the presence of BVD in cell culture.

As discussed in connection with the BVDdN1 virus, attenuated virus characterized by an inactivated N^(pro) protease gene can be incorporated into vaccines and used to induce an immune response in cattle. Dosages and immunization protocols can be optimized so that inoculation of animals results in protective immunity against subsequent viral challenge.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 (panels A and B): panel A shows a schematic representation of the plasmid pVVNADL. This plasmid was mutated to delete the first gene in the open reading frame, i.e., N^(pro) protease. The resulting mutated plasmid product, pBVDdN1. is shown schematically in panel B. Several other gene regions are also shown in FIG. 1. C represents a gene encoding a structural core protein that packages genomic RNA and forms the viral virion. This is followed by genes encoding three envelope glycoproteins—E0, E1 and E2. P7 encodes a nonstructural protein with an unknown function and is followed by a region designated as “NS2-insertion-NS3.” NS2 encodes a highly hydrophobic protein with an zinc finger motif. NS3 is hydrophilic and is a marker of cytopathic BVD virus. Replication of ncp virus in an infected animal can convert the virus into the cp biotype through genetic recombination involving the insertion of an extra viral or cellular RNA sequence between the NS2 and NS3 coding regions. As a result of the recombination, free NS2 and NS3 protein are released. The latter, i.e., NS3, is a protease responsible for most of the nonstructural protein processing that takes place. NS4A is located next to NS3 and is known to encode a cofactor for NS3 protease activity. Following NS4A, there are two genes encoding viral problems, NS4B and NS5A, with unknown functions. The last gene. NS5B, encodes an RNA-dependent RNA polymerase and is responsible for viral replication. The nucleotide sequence (SEQ ID NO:9) shown in panel B is the sequence surrounding the initiation codon of pBVDdN1.

FIG. 2. The complete nucleotide sequence of plasmid pVBDdN1 is shown. The genomic sequence of BVDdN1 is represented by nucleotide 39 to 12,116 (SEQ ID NO:1).

FIG. 3. (Panels A-B) Data demonstrating seroconversion in cattle in response to administration of BVDdN1 virus.

DETAILED DESCRIPTION OF THE INVENTION

A. Production of BVDdN1 and Nucleic Acid Encoding the Virus

The present invention is directed to a BVD virus that has been attenuated by the deletion of the N^(pro) protease gene. The virus has been designed as BVDdN1 and, as suggested by the term “attenuated,” it has been found to replicate at a much slower rate in susceptible cell lines (e.g., bovine testicular cell lines (RD), or bovine kidney cells lines (MDBK)) than its wild type counterpart in vivo. In addition, BVDdN1 does not cause productive infection in embryonic bovine trachea cells (EDTr) or bovine turbinate cells (BT-2), which can be contrasted with the productive infection that occurs following infection with wild type virus. The slow growth of BVDdN1 virus in several different bovine cell lines suggests broad tissue tropism attenuation in animals. BVDdN1 is genetically stable, as the N^(pro) delection is maintained following up to 10 passages in bovine RD cells. Although the genome of the natural virus consists of RNA, this can be reverse transcribed into DNA and cloned. It will be understood that references made herein to nucleic acid and BVD viral sequences encompass both the reverse-transcribed DNA sequences derived from the viral RNA sequences, and the corresponding RNA itself.

The complete nucleotide sequence of the BVDdN1 viral genome is shown in SEQ ID NO:1, from nt 39 to nt 12116. It will be understood that the invention includes not only the viral genomes having the exact sequence shown, but also other sequences that do not differ substantially in terms of structure or function, including, e.g., sequences that encode the same BVD proteins as SEQ ID NO:1 as based on the degeneracy of the genetic code. In addition, e.g., it is well known that techniques such as site-directed mutagenesis can be used to introduce variations into the structure of nucleic acids. Mutations in the BVD virus nucleic acid sequence introduced by this or some similar method, or alternatively by random mutagenesis as known in the art, are encompassed by the invention, provided that at least one major biological characteristic of the resulting virus remains substantially the same as that of the virus from which it was derived. In particular, mutations that do not substantially alter the characteristics of BVDdN1 with respect to infectivity fall within the scope of the invention.

The mutated BVDdN1 nucleic acid was derived from a National Animal Disease Laboratory (NADL) strain of BVD obtained from the American Type Culture Collection (VR-534). This was incorporated into a vector and the full length N^(pro) protease gene was deleted by selective PCR and religation as described in the Examples section below. Although this procedure can be used to obtain the viral genome, and ultimately the virus itself, a plasmid containing the complete BVDdN1 genomic sequence, designated as pBVDdN1, has been deposited as ATCC No. 203354, and the represents the preferred source for isolation procedures. Standard methodology can be used to propagate and purify the plasmid, and transfect it into host cells capable of supporting virus production. The preferred prokaryotic host cell for plasmid propagation is E. coli STBL2 cells (available from GibcoBRL), but other cell types can also be used. The virus can be produced in eukaryotic cells, such as RD or MDBK cells, isolated therefrom in highly purified form using known separation techniques such as sucrose gradient centrifugation, and used in vaccines or to generate antibodies. Alternatively, plasmid can be used to isolate the BVDdN1 genomic sequence and this can be used directly in generating antibodies or in vaccines.

B. The Making of Other Attenuated BVD Viral Strains

The same basic procedure used for generating BVDdN1 virus and genomic nucleic acid can be used in conjunction with other wild type strains of BVD. In each case, the wild type-virus is isolated and attenuation is accomplished by inactivating the N^(pro) protease gene. This can preferably be accomplished by deleting the entire gene using a PCR-based strategy as discussed herein for BVDdN1. However, other methods for inactivating the gene, e.g., by deleting a portion of the sequence or introducing mutations randomly or at specific sites, can also be used. In all cases, the objective is to produce a mutated virus that proliferates at a slow rate after infection. As discussed in the Examples section, infectivity for the virus can be determined in vitro by performing immunohistochemistry using a monoclonal antibody specific for BVD virus.

C. Generation of Antibodies to Attenuated BVD Virus

Antibodies to BVD virus can be produced in any of the animals typically used for antibody production, including mice, rabbits, etc. However, it is preferred that the antibodies be produced in cattle. Compositions containing the virus can be administered to the animals by any route, but typically animals will be injected intramuscularly, subcutaneously or intravenously. Generally, the virus preparation will include an adjuvant, e.g. Freund's complete or incomplete adjuvant. Appropriate preparations for injection, injection schedules and the like are well known in the art and can be employed (see, e.g., Harlow et al., Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, N.Y. (1988); Klein, Immunology: The Science of Self-Nonself Discrimination (1982)). Monoclonal antibodies can also be prepared using standard procedures (Kennett et al., Monoclonal Antibodies and Hybridomas: A New Dimension in Biological Analyses (1980); Campbell, “Monoclonal Antibody Technology” in Laboratory Techniques in Biochemistry and Molecular Biology (1984)).

Antibodies or fragments of antibodies reacting with specificity to BVD virus (i.e., having at least a 100-fold greater affinity for BVD than for any other type of virus) can be used in any of a variety of immunoassays. For example, the antibodies can be used to detect BVD virus in radioimmunoassays or immunometric assays, also known as “two-site” or “sandwich” assays (see Chard, “An Introduction to Radioimmune Assay and Related Techniques,” in Laboratory Techniques in Biochemistry and Molecular Biology, North Holland Publishing Co. N.Y. (1978)). In a typical immunometric assay, a quantity of unlabeled antibody is bound to a solid support that is insoluble in the fluid being tested, e.g., blood, lymph, cellular extracts, etc. After the initial binding of antigen to immobilized antibody, a quantity of detectably labeled second antibody (which may or may not be the same as the first) is added to permit detection and/or quantitation of antigen (see, e.g. Radioimmune Assay Methods, Kirkham et al. ed., pp. 199-206, E&Livingstone Edinburgh (1970)). Many variations of these types of assays are known in the art and can be employed for the detection of BVD virus.

D. Conventional Vaccines and Vaccination Procedures

Vaccines and vaccination procedures employing BVD virus have been discussed in a number of references (see, e.g., Fernelius et al., Am. J. Vet. Res. 33:1421-1431 (1972); Kolar et al., Am. J. Vet. Res. 33:1415-1420 (1972); McClurkin et al., Arch. Virol. 58:119 (1978); Coggins et al., Cornell Vet. 51:539 (1961); Phillips et al., Am. J. Vet. Res. 36:135 (1975); Lobmann et al., Am. J. Vet. Res. 45:2498 (1984); Coria et al., Can. J. Comp. Med. 42;239 (1978); Martin et al., in Proceedings of the Conference Res. Workers Anim. Disc. 75:183 (1994); and U.S. Pat. No. 4,618,493). Typically, a vaccine will contain between about 1×10⁶ and about 1×10⁸ virus particles, with a veterinarily acceptable carrier, in a volume of between 0.5 and 5 ml. Formulation can take place using methods such as those described in Remington's Pharmaceutical Sciences (Mack Publishing Co., Easton, Pa. 16th ed. 1982)). The invention is compatible with various excipients and adjuvants, and these can be incorporated into preparations as desired. For example, vaccine compositions of the present invention can be formulated following accepted convention using standard buffers, carriers, stabilizers, diluents, preservatives, and solubilizers, and can also be formulated to facilitate sustained release. Diluents can include water, saline, dextrose, ethanol, glycerol, and the like. Additives for isotonicity can include sodium chloride, dextrose, mannitol, sorbitol, and lactose, among others. Stabilizers include albumin, among others. Non-limiting examples of adjuvants include the RIBI adjuvant system (Ribi Inc.), alum, aluminum hydroxide gel, oil-in-water emulsions, water-in-oil emulsions such as, e.g., Freund's complete and incomplete adjuvants. Block co polymer (CytRx, Atlanta Ga.), SAF-M (Chiron, Emeryville Calif.) AMPHIGEN® adjuvant, saponin, Quil A, OS-21 (Cambridge Biotech Inc., Cambridge Mass.), or other saponin fractions, monophosphonyl lipid A, Avridine lipid-amine adjuvant, heat-labile enterotoxin from E. coli (recombinant or otherwise), cholera toxin, or muramyl dipeptide, among many others. The vaccine can further comprise one or more other immunomodulatory agents such as, e.g., interleukins, interferons, or other cytokines. Vaccines will generally be designed for parenteral administration, although the present invention is compatible with other forms of administration as well, such as e.g., by oral, intranasal, intramuscular, intra-lymph node, intradermal, intraperitoneal, subcutaneous, rectal or vaginal administration, or by a combination of routes. The skilled artisan will readily be able to formulate the vaccine composition according to the route chosen.

Immunization procedures can be optimized using procedures well known in the art. A single dose can be administered to animals, or, alternatively, two or more inoculations can take place with vaccine separated by intervals of two to ten weeks. If desired, sera can be collected from the inoculated animals and tested for the presence of antibodies to BVD virus.

The terms “induction of an immune response,” and the like, are used broadly herein to include the induction of, or increase in, any immune-based response in cattle in response to vaccination, including either an antibody or cell-mediated immune response, or both, that serves to protect the vaccinated animal against BVD virus. The terms “protective immunity,” “protective immune response,” “protect,”, and the like, as used herein, are not limited to absolute prevention of bovine viral diarrhea in cattle, or absolute prevention of infection of cattle by BVD virus, but are intended to also refer to any reduction in the degree or rate of infection by the pathogen, or any reduction in the severity of the disease or in any symptom or condition resulting from infection with the pathogen as compared to that occurring in an unvaccinated, infected control animal.

E. DNA Vaccines

References describing vaccines and vaccination procedures that utilize nucleic acids (DNA and mRNA) include U.S. Pat. No. 5,703,055, U.S. Pat. No. 5,580,859, U.S. Pat. No. 5,589,466, international Patent Publication WO 98/35562, and various scientific publications, including Ramsay et al., 1997, Immunol. Cell Biol. 75:360-363; Davis, 1997, Cur. Opinion Biotech. 8:635-640; Manickan et al., 1997, Critical Rev. Immunol. 17:139-154, Robinson, 1997, Vaccine 15(8):785-787; Robinson et al., 1996, AIDS Res. Hum. Refr. 12(5):455-457; Lai and Bennet, 1998, Critical Rev. Immunol. 18:449-484; and Vogel and Sarver, 1995, Clin. Microbiol. Rev. 8(3):406-410, which are incorporated herein by reference. These procedures can be utilized can be utilized to produce a vaccine against BVD virus in which nucleic acid corresponding to BVDdN1 nucleic acid, or to a similar BVD viral genome that has been attenuated by the inactivation of the N^(pro) protease gene, or a degenerate variant thereof, is administered to cattle. A vector containing these nucleic acid molecules can also be used immunogens delivered in this manner typically evoke both a humoral and cell-mediated immune response.

Either DNA or RNA encoding the attenuated BVD viral genome can be used in vaccines. The DNA or RNA molecule can be present in a “naked” form or it can be administered together with an agent facilitating cellular uptake (e.g., liposomes or cationic lipids). The typical route of administration will be intramuscular injection of between about 0.1 and about 5 ml of vaccine. Total polynucleotide in the vaccine should generally be between about 0.1 μg/ml and about 5.0 mg/ml. Polynucleotides can be present as part of a suspension, solution or emulsion, but aqueous carriers are generally preferred. Immunization can be accomplished as the result of a single inoculation or due to multiple inoculations. If desired, sera can be collected from the inoculated animals and tested for the presence of antibodies to BVD virus.

The following examples are illustrative only, and are not intended to limit the scope of the present invention.

EXAMPLES Example 1 Assays and Experimental Methods

DNA

The infectious full-length clone pVVNADL is shown schematically in FIG. 1A. This plasmid contains a ColE1 replicon derived from pGEM4 (Promgea Corp.) and is 14,578 bp in length (Vassilev et al., J. Virol. 71:471-478 (1997)). A T7 RNA polymerase promoter is inserted upstream of the BVD viral genome and this promoter can direct wiral RNA synthesis. The sequence of the BVD viral genome was derived from the NADL strain of BVD virus (ATCC VR-534).

Amplification of pVVNADL in E. coli

In general, amplification of the full length pVVNADL clone in E. coli has proven difficult. The deleterious effects of long pestivirus. cDNAs and full-length clones during propagation in E. coli have been noted previously (Moormann et al., J. Virol. 70:763-770 (1996); Rugle et al., J. Virol. 70:3478-3487 (1996)). The stability of pVVNADL was tested in several bacterial hosts including E. coli JM109 (Stratagene); DH5α (GibcoBRL), and STBL2 cells (GibcoBRL). After transformation of plasmid DNA into each of these strains, colony size was monitored and gross plasmic structure was analyzed by restriction mapping. Best results were obtained with STBL2 cells. Transformation of pVVNADL into these cells produced relatively uniform populations of small colonies with no evidence of DNA rearrangement under restricted growth conditions (30° C. for no more than 20 hours) and reasonable DNA yield.

In Vitro Transcription and RNA Transfection

RNA transcripts were synthesized in vitro with T7 RNA polymerase using MEGAscript reagent (Among) according to the manufacturer's protocol. The pVVNADL DNA template was linearized with Sacl and treated with T4 DNA polymerase to remove the 3′ overhang. Transcription reaction products were analyzed by gel electrophoresis 1 to 5 μg of transcript RNA was added to 200 μl of Opti-MEM (GibcoBRL) containing 6 μg of Lipofectin (GibrcoBRL) and RNA/lipid samples were incubated for 10 to 15 minutes at room temperature. During this time, MDBK (a derivative of Madin Darby bovine kidney cells (clone 6)) or RD (a stable transformed bovine testis cell line) monolayers (50 to 60% confluent) grown in 6 well plates (35 mm diameter), were washed twice with RNase-free PBS and once with Opti-MEM. After the final wash, the transfection mixtures were added to each well, which were then incubated for 10 minutes at room temperature with gentle rocking. The wells then received 1 ml Opti-MEM and were incubated for another 3 hours at 37° C. A 3 ml volume of Opti-MEM containing 5% fetal equine serum (for RD cells) or fetal bovine serum (for MDBK cells) was added to each well. Following incubation for 1 to 4 days at 37° C., the cells were fixed with 80% acetone and immunohistochemistry assays were performed to help visualize the BVD virus plaques.

Example 2 Construction of N^(pro) Gene-Deleted BVD Viral Clone

In order to generate a BVD virus with the N^(pro) gene deleted from its genome, three DNA fragments were first generated and the ligated together. The exact procedure is described below.

Generation of PCR Fragment I

“PCR Fragment I” was designed to contain a deletion of the coding sequence of N^(pro). Three PCR amplifications were involved in generating this fragment. In the first, the primers 5NTR3(+) and 5NTR4(−) were used to amplify the half of the 5′NTR region upstream of the N^(pro) coding sequence. The 5′ positive sense primer 5NTR3(+) had the sequence: 5′-AAAGGTCTCGAGATGCCACG-3′ (oligonucleotide 218-237, SEQ ID NO:2). The 3′ negative sense primer 5NTR4)−) had the sequence: 5′-GTCTGACATGTGCCATGTACAG CAGAGATTTTTAGTAGC-3′ (oligonucleotide 895-890+ 388-356, SEQ ID NO:3). Both primers are located in the 5NTR region of the viral genome and the primer 5NTR3(+) contains a unique restriction enzyme site Xhol. Primer 5NTR4(−) contains six extra oligonucleotides at its 5′ end which are homologous to the 5′ end of the coding sequence of the BVD virus C protein. PCR amplification was performed using primers at a final concentration of 0.5 μM, 10 ng of plasmid pVVNADL DNA as template, and 2.5 units of Pfu DNA polymerase (Stratagene, La Jolla, Calif.). Twenty cycles of amplification were performed using the following conditions: denaturation at 94° C. for 30 seconds; annealing at 55° C. for one minute; and extension at 72° C. for two minutes. After purification by agarose gel electrophoresis, the resulting 177 base pair fragment (fragment A) was resuspended in TE buffer.

A second PCR amplification was performed using the oligonucleotides NADLC6(+) and Seq23(−) as primers for amplifying a fragment downstream of the N^(pro) coding sequence. The 5′ positive sense primer NADLC6(+) had the sequence: 5′-CACATGTCAGACACGAAAG AAGAGGGAGC-3′ (oligonucleotides 383-388+890-913. SEQ ID NO:4). The 3′ negative sense primer SEQ23(−) had the sequence 5′-CAGGTTTGCAATCCAAGTGCCCC-3′ (oligonucleotide 2480-2459, SEQ ID NO:5). Primer NADLC6 is located at the N-terminal of protein C. It contains three extra nucleotides homologous to the 3′ and of the 5′ NTR and an initiation codon, ATG, is located at its 5′ end. Primer Se23(−) is located near the N-terminal of protein E2. The plasmid pVVNADL was used as template in the amplification reaction and the conditions were the same as those described above. The resulting DNA fragment (fragment B) was purified by agarose gel electrophoresis and had a size of 1596 bp.

The third amplification was performed using oligonucleotides 5′NTR3(+) (SEQ ID NO:2) and Seq23(−) (SEQ ID NO:5) as primers at a concentration of 0.5 μM, fragments A and B as templates (0.5 μg), and 2.5 units of Pfu DNA polymerase (Stratagena, La Jolla, Calif.). For the first four cycles of amplification, conditions were: denaturation at 94° C. for 30 seconds; annealing at 40° C. for one minute; and extension at 72° C. for two minutes. This was followed by 20 cycles in which conditions were: denaturation at 94° C. for 30 seconds; annealing at 60° C. for one minute; and extension at 72° C. for two minutes. This produced the final product, designated as “PCR Fragment I,” with a size of 1767 bp. This fragment was digested with Xhol and Pvul to form a fragment of 1175 bp before being used for ligation.

Generation of PCR Fragment II

“PCR Fragment II” was generated using the oligonucleotides Seq2(+) and Seq24(−) as primers. The sequence of the 5′ positive sense primer Seq2(+) is as follows: 5′-GGAGCATACGCTGCTTCCCC-3′ (oligonucleotide 1885-1884, SEQ ID NO;6). The 3′-sense primer seq24(−) had the sequence: 5′-GCCTTGCCTATGAGGGAATGG-3′ (oligonucleotide 2963-2942, SEQ ID NO:7). Oligonucleotide Seq2(+) is located near the N-terminal of E1 and oligonucleotide Seq24(−) is located near the middle of the E2 region. Amplification was performed using the plasmid pVVNADL DNA as template under conditions as described above in connection with the amplification using fragments A and B. The resulting fragment, designated as “PCR Fragment II,” had a size of 1098 bp. It was digested with Pvul and Rsrll to form a fragment 929 bp in length before used for ligation.

Generation of Vector Fragment III

The 14579 bp plasmid pVVNADL was digested with Xhol and Rsrll to yield a fragment 11974 bp in length. This was given the designation “Vector Fragment III.”

Generation of Plasmid pBVDN1

PCR Fragments I and II and Vector Fragment III were mixed together at a molecular ratio of 2:2:1 and ligated with 200 units of T4 DNA ligase (Boehringer Mannheim) overnight at 16° C. The ligation product was then transformed into E. coli STBL2 cells and heterologous colonies were screened by mini-DNA purification and specific restriction enzyme digestion. Plasmids having the expected size (14079 bp) were further analyzed by sequence analysis. The resulting plasmid pBVDdN1 is shown in FIG. 1B and contains the expected deletion of the N^(pro) protease gene from BVD viral genome. The vector background for pBVDdN1 is the same as that for pVVNADL.

Example 3 Characterization of N^(pro) Gene-Deleted BVD Viral Clone Infectivity of the N^(pro) Gene-Deleted BVD Viral Clone pBVDdN1

RNA from pBVDdN1 and pVVNADL (positive control) was synthesized in vitro as described previously, and RNA transfection was performed using Lipofectin on RD cell monolayers. At 48, 72 and 96 hours post-transfection, supernatant was collected from the transfected cells and used to reinfect fresh RD monolayers. The transfected cells were fixed with 80% acetone and then examined in an immunohistochemistry assay performed using a Vectastain Elite ABC kit (Vector Laboratories). Monoclonal antibodies used for detecting BVD-specific viral proteins were 15C5 (specific for E0) and CA3 (specific for E2) (Pfizer in-house), although other monoclonal antibodies raised against these antigens can be prepared by standard techniques and used in these same procedures. These antibodies were used of a dilution of 1:1000. Envelope proteins E0 and E2 were detected and virus was produced at 24 hours post-transfection with RNA derived from the parental virus. In contrast, the viral proteins E0 and E2 were first detected at 48 hours post-transfection in cells treated with RNA derived from pBVDdN1. BVDdN1 virus was not rescued until 72 hours post-transfection.

Phenotype Analysis

Early passage BVDdN1 virus stocks (passage 3) were used to inoculate RD and MDBK cell monolayers. These cells were compared with controls inoculated with the parental virus. The cell monolayers were fixed with 80% acetone at 20 hours post-transfection (RD cells) or 24 hours post-transfection (MDBK cells). Fixed cells were then analyzed by immunohistochemistry with the E2-specific monoclonal antibody CA3 at a 1:1000 dilution and examined microscopically. It was found for both cell types that the rate of parental virus replication was significantly faster than the rate of replication exhibited by the BVDdN1 virus.

Genotype Analysis

RNA of both parental virus and BVDdN1 (passage 3) was purified from infected RD monolayers using the Ultraspec™ RNA reagent (Biotect) following the manufacturer's instructions. RT/PCR experiments were performed using RT-PCR beads (Pharmacia Biotech) and the oligonucleotides NADLE07(−) and 5NTR3(+). The sequence and location of the 5NTR3(+) oligonucleotide has been described above. The sequence of oligonucleotide NADLE07(−) is as follows: 5′-CACTTGCATCCATCATACC-3′ (negative sense, oligonucleotide 1379-1361, SEQ ID NO:8). This oligonucleotide is located approximately 150 bp from the N-terminal of E0. It was found that RT/PCR from parental RNA yielded a fragment 1182 bp in size. RT/PCR from BVDdN1 RNA yielded a fragment 661 bp in size, which is as expected for a fragment that had deleted the N^(pro) protease gene. The RT/PCR fragments generated from both parental and BVDdN1 RNA were sequenced. In both cases, the sequence obtained was as expected and corresponded to the arrangement of elements shown in FIG. 1. The complete sequence of BVDdN1 is shown in SEQ ID NO;1 from nt 39 to nt 12116.

Example 4 BVDdN1 Efficacy Study

The purpose of the present study was to evaluate the ability of a vaccine comprising BVDdN1 to cause seroconversion in calves. Fifteen animals (10 for two-dose vaccination with 5 sentinels) were randomly assigned to a first room. Ten other animals were randomly assigned to a second room (one-dose vaccination, no sentinels). BVDdN1 virus was administered to the animals subcutaneously at a dose of 10⁷ TCID₅₀/animal in 2.0 ml MDBK cell lysate. On the days of immunization, the 5 designated sentinel animals were removed from their room. The remaining 10 calves were vaccinated with BVDdN1 virus. Approximately 24 hours post-immunization, the sentinel animal were returned to the treatment room. A second vaccine dose was administered to the first 10 animals in a similar manner approximately 28 days following the first dose.

Rectal temperatures were taken on days −1, 0 (prior to vaccination), 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 (all groups), and on days 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37 and 38 (for animals in the 2-dose group). Blood samples were collected from animals in the 2-dose group on day 0 and weekly thereafter (i.e., on days 7, 14, 21, 28, 35, 42, 49, 56, 63, 70, 77, 84 and 91). Blood samples were collected from animals in the 1-dose group on days 0. 7, 14, 21, 28, 35, 42, 49, 56 and 63.

Serum neutralizing antibodies were detected by SN assay (using BVD virus isolate 5960 for type I, and isolate 890 to type II) to monitor anticipated homologous and heterologous protection.

No significant variations were observed for either general observations or rectal temperatures. None of the sentinel animals servoconverted during the course of the study (data not shown).

All BVDdN1 virus-vaccinated animals servoconverted, as determined by the type I serum neutralization assay. After a single dose vaccination, 80% of animals reached a positive titer of 1:8 or higher at 28 days; and 90% of the animals reached a positive titer of 1:8 or higher at day 35, and subsequently retained a high titer (FIG. 3A). In the type II serum neutralization assay, 70% of the animals were positive at day 63 post-vaccination (data not shown). After a two-dose vaccination, all of the animals reached a positive titer of 1:64 or higher at 7 days, as shown by type I serum neutralization assay, and subsequently maintained a similar seroconversion level (FIG. 3A). For type II serum neutralization assay, most of the animals had a positive titer at 7 days post-second vaccination, and at least 60% of the animals reached a positive titer of 1:8 or above at day 28 (FIG. 3B). These results indicate that BVDdN1 virus is able to replicate in battle and induce a positive neutralization serum for both type-1 and type-2 viruses, which supports the use of this virus as a vaccinal agent for BVDV prevention.

DEPOSIT OF BIOLOGICAL MATERIALS

Plasmid pBVDdN1 was deposited with the American Type Culture Collection (ATCC) at 10801 University Blvd. Manassas, Va., 20110, USA, on Oct. 20, 1998, and was assigned accession number ATCC 203354.

All patents, patent applications, and publications cited above are incorporated herein by reference in their entirety.

The present invention is not limited in scope by the specific embodiments described, which are intended as single illustrations of individual aspects of the invention. Functionally equivalent compositions and methods are within the scope of the invention. Indeed, various modifications of the invention, in addition to those shown and described herein, will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims. 

What is claimed is:
 1. A vaccine comprising an attenuated bovine viral diarrhea virus wherein said virus has a genomic nucleic acid sequence comprising the sequence of SEQ ID NO:1 from nt 39 to nt 12116, or a degenerate variant thereof, wherein said degenerate variant encodes the same amino acid sequence encoded by SEQ ID NO:1 from nt 39 to nt 12116, and a veterinarily acceptable carrier.
 2. A vaccine comprising a nucleic acid molecule comprising the sequence of SEQ ID NO:1 from nt 39 to nt 12116, or a degenerate variant thereof, wherein said degenerate variant encodes the same amino acid sequence encoded by SEQ ID NO:1 from nt 39 to nt 12116, and a veterinarily acceptable carrier.
 3. A vaccine comprising a bovine viral diarrhea (BVD) viral genome made by a method of modifying an isolated with type BVD viral genome for use in a vaccine, comprising mutating the genomic nucleic acid of an isolated with type BVD virus to inactivate the N^(pro) protease gene, and a veterinarily acceptable carrier.
 4. A vaccine comprising an attenuated bovine viral diarrhea (BVD) virus made by a method of attenuating a wild type BVD virus for use in a vaccine, comprising mutating the genomic nucleic acid of said wild type BVD virus to inactivate the N^(pro) protease gene, and a veterinarily acceptable carrier. 